Thank you very much Alessandro for your reply. I guess you are right
regarding this prmtop problem.
The problem arises probably because of the fact that I had a metal (Mn2+)
included with the protein.
Now after taking out the metal, the ba2291_prot.prmtop file is finally
running.
But now I have to treat Mn2+ as a ligand, so I have two ligands ( one is
ATP and another is Mn2+ ion). There is option of only one ligand and a
merged file including both is not running.
Any further suggestion!!!!!!!!!!!!
Saugata
On Wed, Feb 20, 2013 at 3:50 AM, Alessandro Contini <
alessandro.contini.unimi.it> wrote:
> Hi Saugata,
> it looks like a problem in the definition of your .prmtop files. I've
> experienced similar errors (even the segmentation fault you mentioned
> earlier with Amber11 calculation) due to an incorrect definition of masks
> in the input file or unconsistencies with the complex, ligand or receptor
> definitions between the mmpbsa.in and prmtops. I suggest you to carefully
> check your prmtops, in particular ba2291_prot.prmtop as evidenced by the
> attached log.
>
> Regards
>
> Alessandro
>
> Il 20/02/2013 09:08, Saugata Hazra ha scritto:
>
>> Hi All,
>>
>> After getting suggestions from you I have upgraded my AmberTools from
>> AmberTools 1.5 to AmberTools12. But even after doing that I'm getting
>> another error message different from the earlier. I have copied both the
>> error messages. it would be great if you would have suggestions regarding
>> further proceedings.
>>
>> *Error message ** After Upgradation : (When I have Amber 11 with
>> AmberTools 12)*
>>
>> saugata.saugata:~$ cd Desktop/ba2291/mdrun/ba2291_**atp
>> saugata.saugata:~/Desktop/**ba2291/mdrun/ba2291_atp$
>> $AMBERHOME/bin/MMPBSA -O
>> -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp
>> ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
>> bash: /home/saugata/amber12/bin/**MMPBSA: No such file or directory
>> saugata.saugata:~/Desktop/**ba2291/mdrun/ba2291_atp$
>> $AMBERHOME/bin/MMPBSA.py
>> -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp
>> ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
>> Reading command-line arguments and input files...
>> Loading and checking parameter files for compatibility...
>> mmpbsa_py_energy found! Using /home/saugata/amber12/bin/**
>> mmpbsa_py_energy
>> cpptraj found! Using /home/saugata/amber12/bin/**cpptraj
>> Preparing trajectories for simulation...
>> 50 frames were processed by cpptraj for use in calculation.
>>
>> Beginning GB calculations with /home/saugata/amber12/bin/**
>> mmpbsa_py_energy
>> calculating complex contribution...
>> calculating receptor contribution...
>> mmpbsa_py_energy: malloc.c:3801: _int_malloc: Assertion `(unsigned
>> long)(size) >= (unsigned long)(nb)' failed.
>> CalcError: /home/saugata/amber12/bin/**mmpbsa_py_energy failed with
>> prmtop
>> ba2291_prot.prmtop!
>> Exiting. All files have been retained.
>> saugata.saugata:~/Desktop/**ba2291/mdrun/ba2291_atp$
>>
>>
>> *Error message Before Upgradation: (When I had Amber 11 with AmberTools
>> 1.5)
>>
>> *
>> saugata.saugata:~/Desktop/
>> ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA -O -i mmpbsa.in -o
>> FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp ba2291_com.prmtop
>> -rp
>> ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
>> Reading command-line arguments and input files...
>> Loading and checking parameter files for compatibility...
>> ptraj found! Using /home/saugata/amber11/bin/**ptraj
>> mmpbsa_py_energy found! Using /home/saugata/amber11/bin/**
>> mmpbsa_py_energy
>> for GB calculations
>> mmpbsa_py_energy found! Using /home/saugata/amber11/bin/**
>> mmpbsa_py_energy
>> for PB calculations
>> Preparing trajectories for simulation...
>> 50 frames were read in and processed by ptraj for use in calculation.
>>
>> Beginning GB calculations with mmpbsa_py_energy...
>> calculating complex contribution...
>> calculating receptor contribution...
>> Segmentation fault (core dumped)
>> Error: mmpbsa_py_energy error during GB calculations!
>> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
>> --clean to erase these files.
>> saugata.saugata:~/Desktop/**ba2291/mdrun/ba2291_atp$ MMPBSA.py --clean
>> MMPBSA.py: command not found
>> saugata.saugata:~/Desktop/**ba2291/mdrun/ba2291_atp$ MMPBSA --clean
>> Reading command-line arguments and input files...
>> Cleaning temporary files
>> saugata.saugata:~/Desktop/**ba2291/mdrun/ba2291_atp$
>>
>> Thanks,
>> Saugata
>>
>>
>>
>>
>>
>> On Tue, Feb 19, 2013 at 9:43 AM, Jason Swails <jason.swails.gmail.com
>> >wrote:
>>
>> On Tue, Feb 19, 2013 at 9:31 AM, Saugata Hazra <saugata.iitk.gmail.com
>>>
>>>> wrote:
>>>> Thank you very much Jason.
>>>> One more question to make it sure.
>>>> As I have mentioned earlier, that I have Amber 11 & AmberTools 1.5.
>>>> So, is it enough to upgrade only the AmberTool or I also have to upgrade
>>>>
>>> my
>>>
>>>> AMBER to AMBER12.
>>>>
>>>> Upgrading AmberTools is sufficient for MMPBSA.py.
>>>
>>>
>>> Thanks,
>>>> Saugata
>>>>
>>>> On Tue, Feb 19, 2013 at 9:00 AM, Jason Swails <jason.swails.gmail.com
>>>>
>>>>> wrote:
>>>>> On Tue, Feb 19, 2013 at 8:02 AM, Saugata Hazra <saugata.iitk.gmail.com
>>>>>
>>>>>> wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I am running a binding energy calculation (MM-PBSA) for
>>>>>>
>>>>> protein-ligand
>>>
>>>> complex using Amber11 and AmberTools 1.5. I am following Ross Walker
>>>>>> tutorial but have got error message during MMPBSA calculation as
>>>>>>
>>>>> follows:
>>>>
>>>>> saugata.saugata:~/Desktop/**ba2291/mdrun/ba2291_atp$
>>>>>>
>>>>> $AMBERHOME/bin/MMPBSA
>>>>
>>>>> -O
>>>>>> -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop
>>>>>>
>>>>> -cp
>>>
>>>> ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
>>>>>> Reading command-line arguments and input files...
>>>>>> Loading and checking parameter files for compatibility...
>>>>>> ptraj found! Using /home/saugata/amber11/bin/**ptraj
>>>>>> mmpbsa_py_energy found! Using
>>>>>>
>>>>> /home/saugata/amber11/bin/**mmpbsa_py_energy
>>>>
>>>>> for GB calculations
>>>>>> mmpbsa_py_energy found! Using
>>>>>>
>>>>> /home/saugata/amber11/bin/**mmpbsa_py_energy
>>>>
>>>>> for PB calculations
>>>>>> Preparing trajectories for simulation...
>>>>>> 50 frames were read in and processed by ptraj for use in calculation.
>>>>>>
>>>>>> Beginning GB calculations with mmpbsa_py_energy...
>>>>>> calculating complex contribution...
>>>>>> calculating receptor contribution...
>>>>>> Segmentation fault (core dumped)
>>>>>>
>>>>>> Yikes. A segfault from NAB. Try upgrading to AmberTools 12 and use
>>>>>
>>>> that
>>>
>>>> version instead. You can also try putting "use_sander=1" in the
>>>>>
>>>> &general
>>>
>>>> section of the MMPBSA.py input file to force it to use sander instead.
>>>>>
>>>>> Good luck,
>>>>> Jason
>>>>>
>>>>> --
>>>>> Jason M. Swails
>>>>> Quantum Theory Project,
>>>>> University of Florida
>>>>> Ph.D. Candidate
>>>>> 352-392-4032
>>>>> ______________________________**_________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd.org/mailman/listinfo/amber>
>>>>>
>>>>>
>>>>
>>>> --
>>>>
>>>> *Know me Know fun, no me no fun!!!*
>>>> Dr. Saugata Hazra
>>>> ______________________________**_________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd.org/mailman/listinfo/amber>
>>>>
>>>>
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> ______________________________**_________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd.org/mailman/listinfo/amber>
>>>
>>>
>>
>>
>
> --
> Alessandro Contini, PhD
> Dipartimento di Scienze Farmaceutiche
> Sezione di Chimica Generale e Organica "A. Marchesini"
> Via Venezian, 21 20133 Milano
> tel. +390250314480
> e-mail alessandro.contini.unimi.it
> skype alessandrocontini
>
>
--
*Know me Know fun, no me no fun!!!*
Dr. Saugata Hazra
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Received on Sat Feb 23 2013 - 17:00:02 PST
